Freesurfer error while running fMRIPrep command

Software Support
1

Summary of what happened:

I have tried performing an initial preprocessing pipeline using fMRIPrep for data of a single subject, including structural T1- and T2-weighted volumes and rs-fMRI data. However, I get some errors.

Command used (and if a helper script was used, a link to the helper script or the command generated):

fmriprep \
  /home/jovyan/Desktop/dataset/raw \
  /home/jovyan/Desktop/dataset/derivatives \
  participant \
  --output-spaces MNI152NLin2009cAsym \
  --fs-license-file /home/jovyan/Desktop/dataset/license.txt \
  --skip_bids_validation

Version:

fmriprep 25.1.3

Environment (Docker, Singularity / Apptainer, custom installation):

NeuroDesktop

Data formatted according to a validatable standard? Please provide the output of the validator:

Relevant log outputs (up to 20 lines):

	ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0020, pval=0.0000 < threshold=0.0050)

	Manual Talairach alignment may be necessary, or
	include the -notal-check flag to skip this test,
	making sure the -notal-check flag follows -all
	or -autorecon1 in the command string.
	See:

	http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach


	ERROR: Talairach failed!

	Linux d70920d3c5f4 5.15.0-161-generic #171-Ubuntu SMP Sat Oct 11 08:17:01 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux

	recon-all -s sub-032301 exited with ERRORS at Wed Dec 17 19:44:30 UTC 2025

	For more details, see the log file /home/jovyan/Desktop/dataset/derivatives/sourcedata/freesurfer/sub-032301/scripts/recon-all.log
	To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Stderr:

Traceback:
	RuntimeError: subprocess exited with code 1.

Screenshots / relevant information:

2

Hi @Ibai_Azpeitia_Loiti,

This usually indicates a poor quality T1w. Do all images get this error in your study, and have you visualized the T1w?

Best,
Steven

3

Hi @Steven, sorry for the late response.

In my case I was just trying to apply the pipeline to data of a single subject. Viewing the T1w volume of the subject, it could be the case that it is of poor quality, as applying the pipeline to another subject yielded good results.

This is the initial volume i was trying to process.

image
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